After recovering Carmelita's jetpack, Sly Cooper confronts Clockwerk, the malicious fifth member and founder of the Fiendish Five. Clockwerk recognizes Sly's efforts as being remarkable, and stated that the Coopers always found a way to beat him. Surprised, Sly asks how old Clockwerk is, and the mechanical beast arrogantly replies that "Perfection has no age," and explains that his hatred for the Cooper Clan allowed him to live for thousands of years.

Carmelita then informs Sly that her missiles don't hurt Clockwerk, but seem to create holes in his armor, and ordered him to shoot into the gaps she creates. Sly avoids Clockwerk's attacks and causes enough damage that he becomes weakened and falls into the lava below. Clockwerk resurfaces and states that the only reason why he let Sly live when he killed his parents was because he wanted to show the world that without the Thievius Raccoonus, the Cooper line was nothing. Sly replies that the Thievius Raccoonus is a product of great thieves and not the other way around, a sentiment that angers Clockwerk. After a second battle, Clockwerk falls once more, but this time he is severely damaged. Sly has to finish him off before his auto-reconstruct circuitry kicks in.

In Clockwerk's final moments, he tells Sly that he will never be rid of him, and that he is superior. After these last words, Sly hits his damaged head with his cane, decapitating him and ending the Clockwerk menace.

Despite Carmelita saying that blasts from her shock pistol cannot harm Clockwerk, they actually deal a little bit of damage to Clockwerk. It's possible to complete the first two parts of the battle without shooting Clockwerk, though this would take a very long time.